Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1959 |
| PDBID: | 5XJ3 |
| Chains: | DE_F |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.20 |
| Reference: | 10.18632/oncotarget.18004 |
| Antibody | |
| Antibody: | ipilimumab Fv |
| Antibody mutation: | No |
| INN (Clinical Trial): | Danvilostomig(Phase-II); Ipilimumab(Approved); Sovipostobart(Phase-II); |
| Antigen | |
| Antigen: | Cytotoxic T-lymphocyte protein 4 |
| Antigen mutation: | No |
| Durg Target: | P16410 |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >5XJ3_D|Chain A, D, G, J|ipilimumab-VH|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYTMHWVRQAPGKGLEWVTFISYDGNNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVTVSS |
Light Chain: E
Mutation: NULL
| >5XJ3_E|Chain B, E, H, K|ipilimumab-VL|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQSVGSSYLAWYQQKPGQAPRLLIYGAFSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKR |
Antigen
Chain: F
Mutation: NULL
| >5XJ3_F|Chain C, F, I, L|Cytotoxic T-lymphocyte protein 4|Homo sapiens (9606) MKAMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELTFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDPEPCPDSD |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| D: SER30 SER31 THR33 PHE50 SER52 TYR53 ASP54 ASN56 ASN57 TYR59 TRP101 LEU102 GLY103 E: ILE2 GLN27 SER28 GLY30 SER32 TYR33 TYR50 THR57 TYR92 GLY93 SER94 SER95 TRP97 F: LYS36 ALA37 MET38 GLU68 ARG70 THR72 LEU74 GLN76 SER79 VAL81 THR82 GLU83 THR88 ILE128 LYS130 GLU132 MET134 TYR135 PRO137 PRO138 TYR139 TYR140 LEU141 GLY142 ILE143 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
